Rapid discrimination of the native medicinal plant Adenostemma lavenia from its adulterants using PCR-RFLP.

Background: In Taiwan, the aerial part of Adenostemma lavenia (Al) is used in the form of herbal tea or in a folk remedy primarily to mitigate inflammatory conditions in the lungs and liver. Due to the excellent health benefits of Al against inflammation, it has become increasingly crucial and in great demand during the COVID-19 pandemic. However, Al has been found to be adulterated with Wedelia biflora, Sigesbeckia orientalis, and/or Wedelia chinensis because of similarities in appearance and vernacular names. Methods: This study aimed to develop a PCR-RFLP DNA molecular method for the authentication of Al. The restriction enzyme BsrI was used according to the sequencing and alignment results of PCR products in the ITS2 regions of Al and its adulterants. Gel electrophoresis resulted in the clear separation of Al and its adulterants into two distinct categories. Results: In conclusion, the PCR-RFLP authentication method developed herein provides an easy, rapid, and accurate method to distinguish Al from its adulterants to assure user health and safety.

USING DENTAL PATIENT-REPORTED OUTCOMES (dPROs) IN META-ANALYSES: A SCOPING REVIEW AND METHODOLOGICAL INVESTIGATION.

Many studies use dental patient-reported outcomes (dPROs) to evaluate treatments and interventions. However, the consensus on the methodology for combining results of dPROs for meta-analysis has not yet been fully established or widely discussed. The aim of this study is to conduct a scoping review for the methodological issues and difficulties specific to meta-analysis of dPROs and to put forward recommendations for improving quality of meta-analyses of dPRO. We searched the Google Scholar and PubMed databases and identified meta-analysis with dPROs in English. A total of 22 meta-analyses were included in our scoping review, and their characteristics, such as reported outcomes, questionnaires, and effect measures, were extracted. We identified several methodological issues within current literature: (1) synthesizing results from studies with different rating scales; (2) meta-analyses with few studies; (3) the interpretation of standardized mean difference; (4) including studies of different cut-off values in a meta-analysis; and (5) systematic errors due to different instruments. According to each issue mentioned, we provided guidance and recommendations on how to resolve those issues, including using the same Likert scale, conducting an overall and subgroup meta-analysis, using a random-effects model in a meta-analysis, etc. More efforts are required to improve the conduct and interpretation of meta-analyses on dPROs.

R3D-BLAST: a search tool for similar RNA 3D substructures.

R3D-BLAST is a BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea behind R3D-BLAST is that all the RNA 3D structures deposited in the PDB are first encoded as 1D structural sequences using a structural alphabet of 23 distinct nucleotide conformations, and BLAST is then applied to these 1D structural sequences to search for those RNA substructures whose 1D structural sequences are similar to that of the query RNA substructure. R3D-BLAST takes as input an RNA 3D structure in the PDB format and outputs all substructures of the hits similar to that of the query with a graphical display to show their structural superposition. In addition, each RNA substructure hit found by R3D-BLAST has an associated E-value to measure its statistical significance. R3D-BLAST is now available online at http://genome.cs.nthu.edu.tw/R3D-BLAST/ for public access.

FASTR3D: a fast and accurate search tool for similar RNA 3D structures.

FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/.